{"id":"https://openalex.org/W4414593192","doi":"https://doi.org/10.1186/s13321-025-01091-4","title":"Subgrapher: visual fingerprinting of chemical structures","display_name":"Subgrapher: visual fingerprinting of chemical structures","publication_year":2025,"publication_date":"2025-09-29","ids":{"openalex":"https://openalex.org/W4414593192","doi":"https://doi.org/10.1186/s13321-025-01091-4","pmid":"https://pubmed.ncbi.nlm.nih.gov/41024145"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-025-01091-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-01091-4","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-01091-4","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["arxiv","crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-01091-4","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5005557687","display_name":"Lucas Morin","orcid":"https://orcid.org/0000-0002-5829-5118"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]},{"id":"https://openalex.org/I4210126328","display_name":"IBM Research - Zurich","ror":"https://ror.org/02js37d36","country_code":"CH","type":"facility","lineage":["https://openalex.org/I1341412227","https://openalex.org/I4210114115","https://openalex.org/I4210126328"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Lucas Morin","raw_affiliation_strings":["Department of Information Technology and Electrical Engineering, ETH Z\u00fcrich, Sternwartstrasse 7, 8092, Z\u00fcrich, Switzerland. lum@zurich.ibm.com","IBM Research, S\u00e4umerstrasse 4, 8803, R\u00fcschlikon, Switzerland. lum@zurich.ibm.com","IBM Research, S\u00e4umerstrasse 4, 8803, R\u00fcschlikon, Switzerland"],"affiliations":[{"raw_affiliation_string":"Department of Information Technology and Electrical Engineering, ETH Z\u00fcrich, Sternwartstrasse 7, 8092, Z\u00fcrich, Switzerland. lum@zurich.ibm.com","institution_ids":["https://openalex.org/I35440088"]},{"raw_affiliation_string":"IBM Research, S\u00e4umerstrasse 4, 8803, R\u00fcschlikon, Switzerland. lum@zurich.ibm.com","institution_ids":["https://openalex.org/I4210126328"]},{"raw_affiliation_string":"IBM Research, S\u00e4umerstrasse 4, 8803, R\u00fcschlikon, Switzerland","institution_ids":["https://openalex.org/I4210126328"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000851812","display_name":"Gerhard Ingmar Meijer","orcid":null},"institutions":[{"id":"https://openalex.org/I4210126328","display_name":"IBM Research - Zurich","ror":"https://ror.org/02js37d36","country_code":"CH","type":"facility","lineage":["https://openalex.org/I1341412227","https://openalex.org/I4210114115","https://openalex.org/I4210126328"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Gerhard Ingmar Meijer","raw_affiliation_strings":["IBM Research, S\u00e4umerstrasse 4, 8803, R\u00fcschlikon, Switzerland"],"affiliations":[{"raw_affiliation_string":"IBM Research, S\u00e4umerstrasse 4, 8803, R\u00fcschlikon, Switzerland","institution_ids":["https://openalex.org/I4210126328"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037624425","display_name":"Val\u00e9ry Weber","orcid":null},"institutions":[{"id":"https://openalex.org/I4210126328","display_name":"IBM Research - Zurich","ror":"https://ror.org/02js37d36","country_code":"CH","type":"facility","lineage":["https://openalex.org/I1341412227","https://openalex.org/I4210114115","https://openalex.org/I4210126328"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Val\u00e9ry Weber","raw_affiliation_strings":["IBM Research, S\u00e4umerstrasse 4, 8803, R\u00fcschlikon, Switzerland"],"affiliations":[{"raw_affiliation_string":"IBM Research, S\u00e4umerstrasse 4, 8803, R\u00fcschlikon, Switzerland","institution_ids":["https://openalex.org/I4210126328"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5105530582","display_name":"Luc Van Gool","orcid":null},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]},{"id":"https://openalex.org/I58918642","display_name":"Sofia University \"St. Kliment Ohridski\"","ror":"https://ror.org/02jv3k292","country_code":"BG","type":"education","lineage":["https://openalex.org/I58918642"]}],"countries":["BG","CH"],"is_corresponding":false,"raw_author_name":"Luc Van Gool","raw_affiliation_strings":["Department of Information Technology and Electrical Engineering, ETH Z\u00fcrich, Sternwartstrasse 7, 8092, Z\u00fcrich, Switzerland","INSAIT, Sofia University St. Kliment Ohridski, Tsarigradsko shose 111R, 1784, Sofia, Bulgaria"],"affiliations":[{"raw_affiliation_string":"Department of Information Technology and Electrical Engineering, ETH Z\u00fcrich, Sternwartstrasse 7, 8092, Z\u00fcrich, Switzerland","institution_ids":["https://openalex.org/I35440088"]},{"raw_affiliation_string":"INSAIT, Sofia University St. Kliment Ohridski, Tsarigradsko shose 111R, 1784, Sofia, Bulgaria","institution_ids":["https://openalex.org/I58918642"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5024778597","display_name":"Peter Staar","orcid":"https://orcid.org/0000-0002-8088-0823"},"institutions":[{"id":"https://openalex.org/I4210126328","display_name":"IBM Research - Zurich","ror":"https://ror.org/02js37d36","country_code":"CH","type":"facility","lineage":["https://openalex.org/I1341412227","https://openalex.org/I4210114115","https://openalex.org/I4210126328"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Peter W. J. Staar","raw_affiliation_strings":["IBM Research, S\u00e4umerstrasse 4, 8803, R\u00fcschlikon, Switzerland"],"affiliations":[{"raw_affiliation_string":"IBM Research, S\u00e4umerstrasse 4, 8803, R\u00fcschlikon, Switzerland","institution_ids":["https://openalex.org/I4210126328"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5005557687"],"corresponding_institution_ids":["https://openalex.org/I35440088","https://openalex.org/I4210126328"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.27312404,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"17","issue":"1","first_page":"149","last_page":"149"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9975000023841858,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9975000023841858,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12561","display_name":"bioluminescence and chemiluminescence research","score":0.9401000142097473,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/fingerprint","display_name":"Fingerprint (computing)","score":0.7182999849319458},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6147000193595886},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.5835000276565552},{"id":"https://openalex.org/keywords/cheminformatics","display_name":"Cheminformatics","score":0.5063999891281128},{"id":"https://openalex.org/keywords/information-extraction","display_name":"Information extraction","score":0.4325000047683716},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.421099990606308},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.41269999742507935}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7896999716758728},{"id":"https://openalex.org/C2777826928","wikidata":"https://www.wikidata.org/wiki/Q3745713","display_name":"Fingerprint (computing)","level":2,"score":0.7182999849319458},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6147000193595886},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.5835000276565552},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5210999846458435},{"id":"https://openalex.org/C68762167","wikidata":"https://www.wikidata.org/wiki/Q910164","display_name":"Cheminformatics","level":2,"score":0.5063999891281128},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.4325000047683716},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.43149998784065247},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.421099990606308},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.41269999742507935},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.35600000619888306},{"id":"https://openalex.org/C115051666","wikidata":"https://www.wikidata.org/wiki/Q6522493","display_name":"Ranging","level":2,"score":0.35580000281333923},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.3483999967575073},{"id":"https://openalex.org/C168406668","wikidata":"https://www.wikidata.org/wiki/Q178022","display_name":"Fingerprint recognition","level":3,"score":0.3458999991416931},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.34040001034736633},{"id":"https://openalex.org/C52622490","wikidata":"https://www.wikidata.org/wiki/Q1026626","display_name":"Feature extraction","level":2,"score":0.29679998755455017},{"id":"https://openalex.org/C203394866","wikidata":"https://www.wikidata.org/wiki/Q2881060","display_name":"Chemical database","level":2,"score":0.29660001397132874},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.28450000286102295}],"mesh":[],"locations_count":6,"locations":[{"id":"doi:10.1186/s13321-025-01091-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-01091-4","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-01091-4","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmid:41024145","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41024145","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of cheminformatics","raw_type":null},{"id":"pmh:oai:arXiv.org:2504.19695","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2504.19695","pdf_url":"https://arxiv.org/pdf/2504.19695","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:doaj.org/article:c84a9fa559a64dc9800285e456dcae0a","is_oa":true,"landing_page_url":"https://doaj.org/article/c84a9fa559a64dc9800285e456dcae0a","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Cheminformatics, Vol 17, Iss 1, Pp 1-11 (2025)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:11293043","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12482248","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:12482248","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12482248/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Cheminform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13321-025-01091-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-01091-4","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-01091-4","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4414593192.pdf","grobid_xml":"https://content.openalex.org/works/W4414593192.grobid-xml"},"referenced_works_count":31,"referenced_works":["https://openalex.org/W1966456689","https://openalex.org/W1975147762","https://openalex.org/W1988037271","https://openalex.org/W2051810242","https://openalex.org/W2060576972","https://openalex.org/W2096729078","https://openalex.org/W2176758925","https://openalex.org/W2200017991","https://openalex.org/W2219397146","https://openalex.org/W2622206241","https://openalex.org/W2622236128","https://openalex.org/W2905012389","https://openalex.org/W2963150697","https://openalex.org/W2989685001","https://openalex.org/W3007750971","https://openalex.org/W3042595256","https://openalex.org/W3103383152","https://openalex.org/W3130247384","https://openalex.org/W3159789740","https://openalex.org/W3185598321","https://openalex.org/W4306976400","https://openalex.org/W4307468223","https://openalex.org/W4309218736","https://openalex.org/W4313485929","https://openalex.org/W4353112191","https://openalex.org/W4386001223","https://openalex.org/W4390872067","https://openalex.org/W4392094892","https://openalex.org/W4401256332","https://openalex.org/W4408196005","https://openalex.org/W4413156398"],"related_works":[],"abstract_inverted_index":{"Automatic":[0],"extraction":[1],"of":[2,53,101],"molecules":[3,102],"from":[4,17,80],"scientific":[5],"literature":[6],"plays":[7],"a":[8,47,94],"crucial":[9],"role":[10],"in":[11,25,30],"accelerating":[12],"research":[13],"across":[14,122],"fields":[15],"ranging":[16],"drug":[18],"discovery":[19],"to":[20,69],"materials":[21],"science.":[22],"Patent":[23],"documents,":[24],"particular,":[26],"contain":[27],"molecular":[28,72],"information":[29],"visual":[31,51],"form,":[32],"which":[33],"is":[34,108],"often":[35],"inaccessible":[36],"through":[37],"traditional":[38],"text-based":[39],"searches.":[40],"In":[41],"this":[42],"work,":[43],"we":[44],"introduce":[45],"SubGrapher,":[46],"method":[48],"for":[49],"the":[50,99],"fingerprinting":[52,114],"molecule":[54,124],"and":[55,90,103,113,120,125,133],"Markush":[56,104,126],"structure":[57,127],"images.":[58,81],"Unlike":[59],"conventional":[60],"Optical":[61],"Chemical":[62],"Structure":[63],"Recognition":[64],"(OCSR)":[65],"models":[66],"that":[67,97],"attempt":[68],"reconstruct":[70],"full":[71],"graphs,":[73],"SubGrapher":[74,86],"focuses":[75],"on":[76],"extracting":[77],"fingerprints":[78],"directly":[79],"Using":[82],"learning-based":[83],"instance":[84],"segmentation,":[85],"identifies":[87],"functional":[88],"groups":[89],"carbon":[91],"backbones,":[92],"constructing":[93],"substructure-based":[95],"fingerprint":[96],"enables":[98],"retrieval":[100,118],"structures.":[105],"Our":[106],"approach":[107],"evaluated":[109],"against":[110],"state-of-the-art":[111],"OCSR":[112],"methods,":[115],"demonstrating":[116],"superior":[117],"performance":[119],"robustness":[121],"diverse":[123],"depictions.":[128],"The":[129],"benchmark":[130],"datasets,":[131],"models,":[132],"inference":[134],"code":[135],"are":[136],"publicly":[137],"available..":[138]},"counts_by_year":[],"updated_date":"2026-04-13T07:58:08.660418","created_date":"2025-09-29T00:00:00"}
